8PXM | pdb_00008pxm

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(pentane-1,5-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one)

• PDB DOI: https://doi.org/10.2210/pdb8PXM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-23 Released: 2023-10-04 
• Deposition Author(s): Chung, C.W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.309 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Design and Characterization of 1,3-Dihydro-2 H -benzo[ d ]azepin-2-ones as Rule-of-5 Compliant Bivalent BET Inhibitors.

Bamborough, P., Chung, C.W., Goodwin, N.C., Mitchell, D.J., Neipp, C.E., Phillipou, A., Preston, A., Prinjha, R.K., Soden, P.E., Watson, R.J., Demont, E.H.

(2023) ACS Med Chem Lett 14: 1231-1236

• PubMed: 37736196 
• DOI: https://doi.org/10.1021/acsmedchemlett.3c00242
• Primary Citation Related Structures: 
  8PXM, 8PXN


• PubMed Abstract: 
  

  The 1,3-dihydro-2 H -benzo[ d ]azepin-2-ones are potent and ligand-efficient pan-BET bromodomain inhibitors. Here we describe the extension of this template to exploit a bivalent mode of action, binding simultaneously to both bromodomains. Initially the linker length and attachment vectors compatible with bivalent binding were explored, leading to the discovery of exceptionally potent bivalent BET inhibitors within druglike rule-of-5 space.

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Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K.
GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.74 kDa 
• Atom Count: 2,383 
• Modeled Residue Count: 254 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZTY	C [auth A]	(1R)-7-[5-[[(1R)-1,3-dimethyl-2-oxidanylidene-1H-3-benzazepin-7-yl]oxy]pentoxy]-1,3-dimethyl-1H-3-benzazepin-2-one C29 H34 N2 O4 LPZBOHUHUQVYMM-NHCUHLMSSA-N
EDO (Subject of Investigation/LOI)	D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.309 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.936	α = 90
b = 59.766	β = 90
c = 105.287	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Chung, C.W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release